I'd say yes - evidence of mass link building efforts can sometimes hurt rankings rather than help. You might say that you can google-bowl your own rankings.
This Google practice sometimes opens the door to your competitors being able to hurt your rankings, under some situations. The competitive situation isn't that simplistic, and Google does work to limit the possibility - but they also acknowledge it by saying that "There's ALMOST nothing a competitor can do to harm your ranking..."
The directories could certainly be the culprit if they are the 'SEO friendly type' and identical anchors and descriptions were used.
You could have destroyed trust in your site with a bunch of crummy links, but the trust can come back with time. I've even seen cases where the site came back a bit stronger than before, but as I stopped using these sort of links some time ago I can't say if this is still the case. Google might not be so forgiving these days.
I was testing impact of Social media submission on one of my site from a about a month where I selected 10 URL with specific keywords for each page. Then we start submission of each URL in 100 Social sites (2 URL's per week).
I found that as we started to submit the URL/same keywords, the keywords started to drop in SERP's from page#1 to Page #2, #3 and sometimes even #5. ( Note: All 10 keywords were ranking on page#1 for their respective URLs). I some cases the keyword rank stayed, but the URL was removed from the ranking.
However, due to the authority of the site, the ranks were all back within 2 weeks, but for me a complete NO to Social submission for sites hereon.
Absolutely it can hurt, especially if someone simply submits 100 of the exact same keyword anchors to the website all in one fail swoop.
Lesson learned. I see my site come back up one again on spot #8, but now it's gone from the top 100 again. What are the chances that it will come back?
learned this lesson the hard way myself. easiest thing to know what is good or bad is to type "search engine submission service" into Google. Whatever services are being touted on that page (either natural or paid listings) don't do those! ;)
I already learned my lessons on submitting to social media sites. I will not use social media submissions because it has hurt my site before.
For the link development, you need to know about stage of website, if you are new website and it is impossible to get the thousand links in few days, or spike up immediately which seems not look natural, for the establish site, it may be consistent linking not like , some site not get back for a while but suddenly got thousand links in one day.